3 Answers
3

I haven't tried it myself, mind -- but I've seen more than one engineer start building a dispenser, hopping on top of it while it's still propping itself up, then using the extra boost to deposit a teleporter exit on a ledge they couldn't otherwise get to. Maybe that's what's happening?

Engineers can climb to great heights by using the Wrangler. You sit on top of your turret, jump, and have the turret fire at your feet, propelling you to previously unreachable heights. This is how Engineer nests get set up on the small walkway across from the roof that sits over the second checkpoint, on Badwater (Payload). The Engineer will take damage from this, so caution is required to avoid killing yourself.

I've done this plenty of times, at least at one of the circles you indicated.
In the first pic, on the left side, I just jump up on the barrels
There are barrels situated beside the little roof indent, jump on to those.

Then, across on the opposite wall are some crates, jump across to those.

Finally get your TP exit ready, and jump back at the little roof, and place the TP when you can.

I have not done it on the other side (right of first pic) but I assume it would be something similar.

Other than that, the other way I get to different places would be to build my dispenser and jump on it. Now normally you slide off the dispenser, but if you crouch just before you land on it, you stand on top of it. This can push you up to new places such as those you circled on this map, as well as many others on other maps. (My favourite place to do this is in turbine)

"Normally you phase through the dispenser"... Wat? Engineers always clip on their own dispensers, as do enemy players. There is no trick to it. In fact, being able to avoid clipping on a dispenser would be a massive exploit, as you could use it to shield your back from spies.
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LawtonJun 13 '12 at 16:08

Sorry, I mean "normally you fall off the dispenser". Crouching makes you stick to it. If you simply jump on it you will slide off. I'll edit that so the wording is more clear.
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hammythepigJun 13 '12 at 16:16